Integrated analysis of genome-wide genetic and epigenetic association data for identification of disease mechanisms

CpG methylation of the GPX3 promoter in patients with Kashin-Beck Disease potentially promotes chondrocyte apoptosis

OBJECTIVE

To determine the methylation levels of CpGs in the GPX3 promoter region and explore their potential effects on the apoptosis of chondrocytes.

METHODS

Blood specimens were collected from 32 participants; 16 KBD patients and 16 healthy subjects. Twenty-five CpGs in the promoter region of GPX3 were identified and detected by MALDI-TOF-MS. Methylation levels of CpGs were compared between KBD patients and healthy subjects as well as among the KBD patients with different degrees. C28/I2 human chondrocytes were treated with tBHP and Na2SeO3. Apoptosis in chondrocytes was examined under a fluorescence microscope.

RESULTS

The methylation levels of GPX3-1_CpG_11 and GPX3-1_CpG_16 in KBD patients were significantly higher than those of healthy subjects (P < 0.05). The methylation levels of the other CpGs were not significantly different between the two groups (P > 0.05). The methylation level of GPX3-1_CpG_24 in KBD patients was significantly higher than those of healthy subjects (P < 0.05). MSP-PCR analysis indicated that the methylation rate of KBD group (9.41%) was significantly higher than that of healthy subjects (1.18%), and that GPX3 DNA methylation increased the risk of acquiring KBD 8 fold (OR = 8.000, 95% CI: 1.023-62.580); The mRNA expression of GPX3 in whole blood of KBD patients was lower than that of healthy subjects (P＜0.05); Compared with the control group, GPX3, GPX1 and GPX4 mRNA level of the tertbutyl hydroperoxide injury group decreased significantly (P < 0.05), after supplementation with Na2SeO3. The rate of chondrocytes apoptosis was decreased with the increasing of GPX3 and GPX4 mRNA levels (P＜0.05) and GPX3 mRNA showed a similar trend without statistically significant (P＞0.05).

CONCLUSION

The methylation patterns of CpGs in GPX3 varied in KBD patients. The experiments indicated that the increased methylation of CpGs within the GPX3 promoter may down-regulate the expression of GPX3, thereby reducing the antioxidant function of GPX3 and promoting chondrocyte apoptosis, both of which accelerates the occurrence of KBD. We therefore propose a new understanding of GPX3's potential epigenetic and genetic mechanisms that contribute to KBD.

Air pollution and meteorological conditions during gestation and type 1 diabetes in offspring

BACKGROUND

Growing evidence indicates that air pollution is capable of disrupting the immune system and therefore, might be associated with an onset of Type 1 diabetes (T1D).

OBJECTIVES

We explored possible links of T1D with ambient exposures in the population of southern Israel, characterized by hot and dry climate and frequent dust storms.

METHODS

We conducted a matched nested case-control study where exposure to environmental pollutants during gestation in T1D cases was compared to that of healthy children. Up to 10 controls were matched to every case by age, gender and ethnicity, in all 362 cases and 3512 controls. Measurements of pollutants' concentrations, nitrogen dioxide (NO₂), sulphur dioxide (SO₂), ozone (O₃) and particulate matter of size less than 10 and 2.5 μm in diameter (PM₁₀ and PM_2.5), as well as the mean daily measurements of meteorological conditions were obtained from the local monitoring stations. The association between T1D and pollution, solar radiation (SR), temperature and relative humidity was adjusted for socioeconomic status, temperature, maternal age and pre-gestational maternal DM, using conditional logistic regression. The environmental exposures were presented as indicators of quartiles averaged over whole pregnancy and by trimesters.

RESULTS

Exposure to ozone and solar radiation during gestation were both associated with the T1D in offspring, although at borderline significance. Compared to the lowest quartile, the odds ratio (OR) for exposure to 3rd and 4th quartile of O₃ was equal 1.61 (95%CI: 0.95; 2.73) and 1.45 (95%CI: 0.83; 2.53), respectively. Likewise, the ORs for exposure to SR were equal 1.83 (95%CI: 0.92; 3.64), 2.54 (95%CI: 1.21; 5.29) and 2.06 (95%CI: 0.95; 4.45) for to 2nd, 3rd and 4th quartiles, respectively. Exposure to SO₂ followed a dose-response pattern, but was not statistically significant. Other environmental factors were not independently related to T1D. Analysis of exposures one year prior to the disease onset indicated a positive association between T1D and SR.

CONCLUSIONS

We showed that exposure to high ozone levels and solar radiation during gestation might be related to the T1D. More scientific evidence needs to accumulate to support the study findings.

Harsh Parenting Predicts Novel HPA Receptor Gene Methylation and NR3C1 Methylation Predicts Cortisol Daily Slope in Middle Childhood

Adverse experiences in childhood are associated with altered hypothalamic-pituitary-adrenal (HPA) axis function and negative health outcomes throughout life. It is now commonly accepted that abuse and neglect can alter epigenetic regulation of HPA genes. Accumulated evidence suggests harsh parenting practices such as spanking are also strong predictors of negative health outcomes. We predicted harsh parenting at 2.5 years old would predict HPA gene DNA methylation similarly to abuse and neglect, and cortisol output at 8.5 years old. Saliva samples were collected three times a day across 3 days to estimate cortisol diurnal slopes. Methylation was quantified using the Illumina Infinium MethylationEPIC array BeadChip (850 K) with DNA collected from buccal cells. We used principal components analysis to compute a summary statistic for CpG sites across candidate genes. The first and second components were used as outcome variables in mixed linear regression analyses with harsh parenting as a predictor variable. We found harsh parenting significantly predicted methylation of several HPA axis genes, including novel gene associations with AVPRB1, CRHR1, CRHR2, and MC2R (FDR corrected p < 0.05). Further, we found NR3C1 methylation predicted a steeper diurnal cortisol slope. Our results extend the current literature by demonstrating harsh parenting may influence DNA methylation similarly to more extreme early life experiences such as abuse and neglect. Further, we show NR3C1 methylation is associated with diurnal HPA function. Elucidating the molecular consequences of harsh parenting on health can inform best parenting practices and provide potential treatment targets for common complex disorders.

Association of CNVs with methylation variation

Germline copy number variants (CNVs) and single-nucleotide polymorphisms (SNPs) form the basis of inter-individual genetic variation. Although the phenotypic effects of SNPs have been extensively investigated, the effects of CNVs is relatively less understood. To better characterize mechanisms by which CNVs affect cellular phenotype, we tested their association with variable CpG methylation in a genome-wide manner. Using paired CNV and methylation data from the 1000 genomes and HapMap projects, we identified genome-wide associations by methylation quantitative trait locus (mQTL) analysis. We found individual CNVs being associated with methylation of multiple CpGs and vice versa. CNV-associated methylation changes were correlated with gene expression. CNV-mQTLs were enriched for regulatory regions, transcription factor-binding sites (TFBSs), and were involved in long-range physical interactions with associated CpGs. Some CNV-mQTLs were associated with methylation of imprinted genes. Several CNV-mQTLs and/or associated genes were among those previously reported by genome-wide association studies (GWASs). We demonstrate that germline CNVs in the genome are associated with CpG methylation. Our findings suggest that structural variation together with methylation may affect cellular phenotype.

Constructing an integrated genetic and epigenetic cellular network for whole cellular mechanism using high-throughput next-generation sequencing data

Background

Epigenetics has been investigated in cancer initiation, and development, especially, since the appearance of epigenomics. Epigenetics may be defined as the mechanisms that lead to heritable changes in gene function and without affecting the sequence of genome. These mechanisms explain how individuals with the same genotype produce phenotypic differences in response to environmental stimuli. Recently, with the accumulation of high-throughput next-generation sequencing (NGS) data, a key goal of systems biology is to construct networks for different cellular levels to explore whole cellular mechanisms. At present, there is no satisfactory method to construct an integrated genetic and epigenetic cellular network (IGECN), which combines NGS omics data with gene regulatory networks (GRNs), microRNAs (miRNAs) regulatory networks, protein-protein interaction networks (PPINs), and epigenetic regulatory networks of methylation using high-throughput NGS data.

Results

We investigated different kinds of NGS omics data to develop a systems biology method to construct an integrated cellular network based on three coupling models that describe genetic regulatory networks, protein–protein interaction networks, microRNA (miRNA) regulatory networks, and methylation regulation. The proposed method was applied to construct IGECNs of gastric cancer and the human immune response to human immunodeficiency virus (HIV) infection, to elucidate human defense response mechanisms. We successfully constructed an IGECN and validated it by using evidence from literature search. The integration of NGS omics data related to transcription regulation, protein-protein interactions, and miRNA and methylation regulation has more predictive power than independent datasets. We found that dysregulation of MIR7 contributes to the initiation and progression of inflammation-induced gastric cancer; dysregulation of MIR9 contributes to HIV-1 infection to hijack CD4+ T cells through dysfunction of the immune and hormone pathways; dysregulation of MIR139-5p, MIRLET7i, and MIR10a contributes to the HIV-1 integration/replication stage; dysregulation of MIR101, MIR141, and MIR152 contributes to the HIV-1 virus assembly and budding mechanisms; dysregulation of MIR302a contributes to not only microvesicle-mediated transfer of miRNAs but also dysfunction of NF-κB signaling pathway in hepatocarcinogenesis.

Conclusion

The coupling dynamic systems of the whole IGECN can allow us to investigate genetic and epigenetic cellular mechanisms via omics data and big database mining, and are useful for further experiments in the field of systems and synthetic biology.

Type I diabetes in paediatric age in Apulia (Italy): Incidence and associations with outdoor air pollutants

AIM

This study aimed to explore Type 1 diabetes (T1D) incidence and possible relations with specific air pollutants in a large population of children, during a wide time period.

METHODS

T1D rates and trends were examined (2001-2013, GAM and Joinpoint Regression analysis) by data on the first hospitalization in all children (0-14 years) living in Apulia (Southern Italy, average yearly population aged 0-14 years in the examined period: 631,275 subjects), and linked with levels of PM10, NOx, CO and ozone.

RESULTS

A total of 1501 children were first discharged in the selected area with a diagnosis of T1D. Incidence decreased from 48.5 (95% CI 43.3; 54.0, 2001) to 16.9 per 100,000 (95% CI 13.7; 20.6, 2013), with differences according to age at onset (constant at 0-4 years, continuously decreasing at 5-9 years, decreasing until 2003 at 10-14 years), and with a positive relation with PM10--but not ozone, NOx and CO average air levels. The OR was 1.037 (1.002; 1.074) in the high tertile of PM10 concentrations, and mean incidence was higher with PM10 levels in the highest, than in the medium/reference tertile. Mean age at T1D onset was linked with yearly PM10 and ozone air levels.

CONCLUSIONS

On a wide period, a stable or decreased incidence of T1D was evident in children with early- or later onset of disease, respectively. PM10 exposure significantly affects the incidence of T1D, which might be considered, at least in part, a preventable condition.

Next-generation sequencing and epigenomics research: a hammer in search of nails

After the initial enthusiasm of the human genome project, it became clear that without additional data pertaining to the epigenome, i.e., how the genome is marked at specific developmental periods, in different tissues, as well as across individuals and species-the promise of the genome sequencing project in understanding biology cannot be fulfilled. This realization prompted several large-scale efforts to map the epigenome, most notably the Encyclopedia of DNA Elements (ENCODE) project. While there is essentially a single genome in an individual, there are hundreds of epigenomes, corresponding to various types of epigenomic marks at different developmental times and in multiple tissue types. Unprecedented advances in next-generation sequencing (NGS) technologies, by virtue of low cost and high speeds that continue to improve at a rate beyond what is anticipated by Moore's law for computer hardware technologies, have revolutionized molecular biology and genetics research, and have in turn prompted innovative ways to reduce the problem of measuring cellular events involving DNA or RNA into a sequencing problem. In this article, we provide a brief overview of the epigenome, the various types of epigenomic data afforded by NGS, and some of the novel discoveries yielded by the epigenomics projects. We also provide ample references for the reader to get in-depth information on these topics.

Functional interpretation of non-coding sequence variation: concepts and challenges

Understanding the functional mechanisms underlying genetic signals associated with complex traits and common diseases, such as cancer, diabetes and Alzheimer's disease, is a formidable challenge. Many genetic signals discovered through genome-wide association studies map to non-protein coding sequences, where their molecular consequences are difficult to evaluate. This article summarizes concepts for the systematic interpretation of non-coding genetic signals using genome annotation data sets in different cellular systems. We outline strategies for the global analysis of multiple association intervals and the in-depth molecular investigation of individual intervals. We highlight experimental techniques to validate candidate (potential causal) regulatory variants, with a focus on novel genome-editing techniques including CRISPR/Cas9. These approaches are also applicable to low-frequency and rare variants, which have become increasingly important in genomic studies of complex traits and diseases. There is a pressing need to translate genetic signals into biological mechanisms, leading to prognostic, diagnostic and therapeutic advances.